These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Once Acceptable Targets: Lesbians and transmen, if Sam's smart-ass comments to Brahma (nee Madeleine) are any example.
Then, the whole point of the rebellion is that they aren't actually gods and he's sick of pretending to be. Having elements of bigotry in his thinking and a plethora of sexual hang-ups is about as human as it gets.
Also Sam is tired of keeping of the charade of being something they're not (even pretending to be Buddha annoys him), and Sam's comments are more like calling out Brahma/Madeleine of his/her own hatred of his/her own femininity.
Strawman Has a Point: Though they use it to justify their control over humanity, "gods" have a point: humanity is not prepared for progress, as science, used in wrong way, can really destroy and pollute the planet. Knowing that the first ones were survivors from detroyed Earth, they maybe somewhat right.
It's ambiguous as to whether or not Earth was actually destroyed or if the Star of India just couldn't get back to it. Also, the "humans aren't ready for Science" angle is a poor excuse at best when you consider that the gods are the ones responsible for the lack of knowledge and technology among the common man, not for environmental purposes but to keep their worshipers from being able to question or depose them.